Contacts of the helix formed by residues 113 - 121 (chain L) in PDB entry 1RBO
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with VAL 113 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111L GLY 4.0 0.8 + - - -
112L SER* 1.3 71.9 - - - +
114L THR* 1.3 61.7 + - - +
116L MET* 3.2 14.0 + - + +
117L PHE* 3.0 31.9 + - + +
148L PHE* 3.6 23.6 - - + -
274L PHE* 3.6 37.7 - - + -
278L THR* 5.5 4.0 + - - +
317L ALA* 3.7 34.8 - - + +
320L LEU* 4.0 11.0 - - + -
321L SER* 4.1 9.9 - - - +
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Residues in contact with THR 114 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112L SER* 3.1 8.5 - - - +
113L VAL* 1.3 79.6 - - - +
115L ASN* 1.3 57.8 + - - +
117L PHE* 3.6 3.3 + - - +
118L THR* 2.7 39.1 + - - +
274L PHE* 3.4 24.4 - - - +
275L THR* 3.1 26.6 + - - +
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Residues in contact with ASN 115 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107L LEU 3.8 7.1 + - - +
108L PHE* 3.4 12.3 - - - +
109L GLU* 2.9 38.2 + - + +
112L SER* 3.1 26.5 + - - +
114L THR* 1.3 76.3 - - - +
116L MET* 1.3 67.5 + - - +
118L THR* 3.2 18.1 + - - +
119L SER* 3.3 18.9 + - - -
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Residues in contact with MET 116 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36L ILE* 5.2 5.8 - - + -
108L PHE* 3.8 18.2 - - + -
112L SER 3.2 13.1 + - - +
113L VAL* 3.2 20.8 + - + +
115L ASN* 1.3 77.8 + - - +
117L PHE* 1.3 86.2 + - + +
119L SER* 3.5 1.6 + - - -
120L ILE* 3.2 40.6 + - + +
138L LEU* 4.1 17.3 - - + -
140L ILE* 4.6 13.9 - - + -
144L TYR* 4.0 28.2 + - - +
317L ALA* 4.9 4.3 - - + +
320L LEU* 4.5 17.3 - - + -
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Residues in contact with PHE 117 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113L VAL* 3.0 17.4 + - + +
114L THR* 4.2 3.1 - - - +
116L MET* 1.3 94.7 - - + +
118L THR* 1.3 66.6 + - - +
120L ILE* 4.9 2.5 - - + -
121L VAL* 2.9 38.9 + - + +
122L GLY* 3.3 4.2 + - - -
135L LEU* 5.2 1.1 - - + -
138L LEU* 4.3 6.1 - - + -
274L PHE* 3.5 41.5 - + + -
309L MET* 3.8 26.2 - - + -
313L VAL* 3.8 24.7 - - + -
314L LEU* 4.3 6.3 - - + -
317L ALA* 3.6 22.9 - - + -
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Residues in contact with THR 118 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114L THR* 2.7 30.9 + - - +
115L ASN* 3.2 13.1 + - - +
117L PHE* 1.3 75.7 - - - +
119L SER* 1.3 59.6 + - - +
122L GLY* 3.1 29.0 + - - +
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Residues in contact with SER 119 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61L SER* 3.2 36.8 + - - -
62L SER* 5.8 0.3 - - - -
103L TYR* 5.8 0.4 - - - -
107L LEU* 4.7 12.7 + - - +
108L PHE* 4.3 16.5 - - - -
115L ASN* 3.3 14.8 + - - -
116L MET 3.9 6.1 - - - -
117L PHE 3.2 0.2 - - - -
118L THR* 1.3 84.0 - - - +
120L ILE* 1.3 66.7 + - - +
121L VAL 3.3 0.5 + - - -
122L GLY* 3.7 3.1 + - - -
123L ASN 5.1 1.7 + - - -
124L VAL* 5.6 0.2 - - - +
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Residues in contact with ILE 120 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36L ILE* 3.9 18.2 - - + -
38L ALA* 4.5 0.2 - - + -
40L PHE* 3.6 35.2 - - + -
61L SER* 4.1 8.4 - - - -
103L TYR* 4.0 22.2 - - + +
108L PHE* 4.1 13.5 - - + -
116L MET* 3.2 31.6 + - + +
117L PHE* 4.6 2.7 - - + +
119L SER* 1.3 77.0 - - - +
121L VAL* 1.3 58.3 - - + +
124L VAL* 3.6 11.6 - - - +
135L LEU* 4.1 20.9 - - + -
138L LEU* 3.7 27.6 - - + -
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Residues in contact with VAL 121 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40L PHE* 5.0 0.2 - - + -
117L PHE* 2.9 28.7 + - + +
120L ILE* 1.3 77.2 - - + +
122L GLY* 1.3 66.2 + - - +
123L ASN 3.7 1.5 + - - -
124L VAL* 5.0 0.4 - - - -
125L PHE* 3.4 45.6 + - + +
135L LEU* 3.9 24.9 - - + -
309L MET* 3.9 26.7 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il